New York Clinical Laboratory Requirements

New York runs the most demanding state laboratory program in the country — many labs treat a New York permit as the gold standard. If your lab is in New York, or if you're an out-of-state lab testing specimens from New York patients, you need a New York clinical laboratory permit before you perform a single patient test.

State agency

New York State Department of Health, Wadsworth Center, Clinical Laboratory Evaluation Program (CLEP) — the office that issues clinical laboratory permits. Individual testing personnel are licensed through the NYSED Office of Professions.

License types

Clinical laboratory permit — issued by category of testing; application and inspection/reference fees apply — see CLEP's laboratory fee page for the current schedule (fees are invoiced based on gross annual receipts).
Limited service laboratory registration — for extension sites offering waived or provider-performed microscopy procedures (form DOH-4081), applied for after the main permit is issued.
Out-of-state permit — required for any out-of-state laboratory testing specimens from New York patients. Non–New York corporations must also be authorized to do business in New York by the Secretary of State before applying.

How to apply

Apply through CLEP's eCLEP portal with the permit application, disclosure of ownership, HCS affiliation forms, and management contracts where applicable. Before patient testing can begin, the lab must: complete an initial on-site survey, participate in required proficiency testing, and — for laboratory-developed tests — obtain explicit Department approval of the test through CLEP's test-approval process. Out-of-state laboratories should budget for survey travel expenses, which the lab pays and which are billed after the survey.

Forms

Application forms — apply through the CLEP eCLEP portal; paper forms and instructions below.

DOH-3494 (Clinical Laboratory Permit Application) — the permit application, filed via eCLEP; get the current form and instructions from the CLEP obtain-a-permit page.
DOH-4081 (Application for Limited Service Laboratory) — registration for waived/PPM extension sites; same page.
CLEP permit application instructions (PDF) — step-by-step instructions for the initial permit application.
Certificate of Qualification initial application (PDF) — for laboratory directors ($150 application fee).
Form CMS-116 — CLIA Application for Certification (PDF) — New York is a CLIA-exempt state; in-state labs are assigned a CLIA number by CLEP, but out-of-state applicants should have theirs ready.

Inspection preparedness — have these ready before the surveyors arrive:

Form CMS-116 — CLIA Application for Certification (PDF) — surveyors verify the specialties, sites, and director on file match current operations.
Form CMS-209 — Laboratory Personnel Report (PDF) — current personnel roster; surveyors require it up to date.
Updated Lab Test Menu — the lab's controlled test menu listing every test by specialty; surveyors cross-check it against the certificate.
NYSDOH Clinical Laboratory Standards of Practice, Part 1 — General Systems (PDF) — the standards surveys are graded against; build your quality system to them.
CLEP on-site survey process — what the mandatory pre-permit survey covers.
CLEP proficiency testing provider search — find PT surveys that meet New York's requirements.
CLEP Proficiency Testing Guide (PDF) — how CLEP evaluates PT participation.

Fees

Annual permit fees apply; survey expenses for in-state laboratories are included in those fees. Out-of-state laboratories pay survey travel costs separately. The laboratory director's Certificate of Qualification carries a $150 application fee. Check CLEP's current fee page before filing.

Personnel requirements

New York licenses laboratory personnel individually. Technologists and technicians are licensed through the NYSED Office of Professions, and laboratory directors must hold a Certificate of Qualification from CLEP. Personnel performing remote testing activities must be licensed in the state where the work is performed.

Inspection

An initial on-site survey is required before a permit is issued and before any patient testing. Out-of-state surveys are announced; subsequent routine surveys of in-state laboratories are unannounced. The survey checks premises, laboratory practice, equipment, personnel, and record-keeping against state law and the New York State Clinical Laboratory Standards of Practice.

Renewal and changes

Permits renew annually. Report changes — including director changes, which require the new director to be granted access to the state's Health Commerce System — to CLEP promptly so the permit record stays current.

How New York differs from federal CLIA

A New York permit is required in addition to the CLIA certificate, and no patient testing may begin before the permit is issued.
Out-of-state labs need a New York permit to test New York patient specimens — plus authorization to do business in New York.
An on-site survey is mandatory before permitting, and out-of-state labs pay the surveyors' travel expenses.
Laboratory-developed tests need explicit Department approval before use.
Individual personnel licensure for technologists, technicians, and directors.

Official links

Last verified: October 2026